https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1344-7

Address of the bookmark: http://ufmg-simba.sourceforge.net/

The data are available using NCBI accession IDs: BioProject: (PRJNA483067), assembly: [RBJD00000000] and sequence data (SRP155659).

Additional Resources

• Interactive map showcasing global initiatives underway to generate reference-quality human genome assemblies for diverse populations
• BioReport Podcast on the value of ethnic-specific reference genomes
• Nature Reviews Genetics paper from NHGRI: Prioritizing diversity in human genomics research
• Article in The Journal of Precision Medicine: “Minority Report – Ethnic Diversity and the Real Promise for Precision Medicine”
• Article in Bio-IT World: “Genomic Data Standards Are a Necessity”
• NHGRI Project Award: High Quality Human and Non-Human Primate Genome Assemblies

More details are available on the PacBio website:

• Blog post: Data Release: Highest-Quality, Most Contiguous Individual Human Genome Assembly to Date
• Blog post: For Reference-Grade Human Genome Assemblies, SMRT Sequencing Yields Optimal Results
• Webinar:  Assembling High-Quality Human Reference Genomes for Global Populations
• FALCON-Phase press release and article preprint
• PacBio research focus webpage about Human Population Genetics

 Ref: https://stockguru.com/2018/10/08/pacific-biosciences-releases-highest-quality-most-contiguous-individual-human-genome-assembly-to-date/

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.

Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting.

Therefore, Genobuntu offers a well-tailored environment for both novices and experts working in the field of genome assembly.

Address of the bookmark: https://sourceforge.net/projects/genobuntu/

https://academic.oup.com/bib/article/22/3/bbaa123/5868070

Address of the bookmark: https://github.com/hzi-bifo/Quasimodo

Address of the bookmark: https://proksee.ca/

Address of the bookmark: https://github.com/bcgsc/ARCS/

We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep sequencing platform <ftp://webdata:webdata@ussd-ftp.illumina.com/Data/SequencingRuns/NA18507_GAIIx_100_chr21.bam>, aligned to the b36/hg18 reference genome)

Address of the bookmark: https://wiki.bits.vib.be/index.php/NGS_Exercise.6#compare_aln_.26_mem_results_with_vcf-compare

Once a query gene has been entered, it is displayed in its genomic context in parallel to the genomic context of all its orthologous and paralogous copies in all the other sequenced metazoan genomes. Moreover, Genomicus stores and displays the predicted ancestral genome structure in all the ancestral species within the phylogenetic range of interest.

All the data on extant species displayed in this browser are from Ensembl.

Summary statistics of Genomicus version 105.01: (view species tree in pdf or newick)

Address of the bookmark: https://www.genomicus.bio.ens.psl.eu/genomicus-105.01/cgi-bin/search.pl

• paired-end (PE) and/or mate-pair libraries (NGS-based mode)
• long reads (NGS-based mode)
• synteny to the genome of some related species (reference-based mode)

Scaffolding 

In reference-based mode, pyScaf uses synteny to the genome of closely related species in order to order contigs and estimate distances between adjacent contigs.

Contigs are aligned globally (end-to-end) onto reference chromosomes, ignoring:

• matches not satisfying cut-offs (--identity and --overlap)
• suboptimal matches (only best match of each query to reference is kept)
• and removing overlapping matches on reference.

In preliminary tests, pyScaf performed superbly on simulated heterozygous genomes based on C. parapsilosis (13 Mb; CANPA) and A. thaliana (119 Mb; ARATH) chromosomes, reconstructing correctly all chromosomes always for CANPA and nearly always for ARATH (Figures in dropbox, CANPA table, ARATH table).
Runs took ~0.5 min for CANPA on 4 CPUs and ~2 min for ARATH on 16 CPUs.

Important remarks:

• Reduce your assembly before (fasta2homozygous.py) as any redundancy will likely break the synteny.
• pyScaf works better with contigs than scaffolds, as scaffolds are often affected by mis-assemblies (no de novo assembler / scaffolder is perfect...), which breaks synteny.
• pyScaf works very well if divergence between reference genome and assembled contigs is below 20% at nucleotide level.
• pyScaf deals with large rearrangements ie. deletions, insertion, inversions, translocations. Note however, this is experimental implementation!
• Consider closing gaps after scaffolding.

Address of the bookmark: https://github.com/lpryszcz/pyScaf

Using AlignGraph

AlignGraph --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa --genome genome.fa --distanceLow distanceLow --distanceHigh distancehigh --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa [--kMer k --insertVariation insertVariation --coverage coverage --part p --fastMap --ratioCheck --iterativeMap --misassemblyRemoval --resume]

Address of the bookmark: https://github.com/baoe/AlignGraph